RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Algorithms for phylogenetic footprinting
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Finding motifs using random projections
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
On the closest string and substring problems
Journal of the ACM (JACM)
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
A Statistical Method for Finding Transcription Factor Binding Sites
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Spelling Approximate Repeated or Common Motifs Using a Suffix Tree
LATIN '98 Proceedings of the Third Latin American Symposium on Theoretical Informatics
On the complexity of finding common approximate substrings
Theoretical Computer Science
RISOTTO: fast extraction of motifs with mismatches
LATIN'06 Proceedings of the 7th Latin American conference on Theoretical Informatics
An efficient algorithm for planted structured motif extraction
Proceedings of the 1st ACM workshop on Breaking frontiers of computational biology
Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Faster Algorithms for Sampling and Counting Biological Sequences
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
A simple algorithm for (l, d) motif search
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Swiftly computing center strings
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
A frequent pattern mining method for finding planted (l, d)-motifs of unknown length
RSKT'10 Proceedings of the 5th international conference on Rough set and knowledge technology
An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Optimizing genetic algorithm for motif discovery
Mathematical and Computer Modelling: An International Journal
An improved voting algorithm for planted (l,d) motif search
Information Sciences: an International Journal
| Hi-index | 0.00 |
We consider the planted (l, d) motif search problem, which consists of finding a substring of length l that occurs in a set of input sequences {s1, . . . , sn} with up to d errors, a problem that arises from the need to find transcription factor-binding sites in genomic information. We propose a sequence of practical algorithms, which start based on the ideas considered in PMS1. These algorithms are exact, have little space requirements, and are able to tackle challenging instances with bigger d, taking less time in the instances reported solved by exact algorithms. In particular, one of the proposed algorithms, PMSprune, is able to solve the challenging instances, such as (17, 6) and (19, 7), which were not previously reported as solved in the literature.